Updated October 4th, 2019
AI: Artificial intelligence BIO: Bioinformatic libraries & apps CHEM: Chemistry libraries & app GEO: Geography libraries & apps IO: Input/output software
M: MPI implementations MATH: Mathematical libraries PHYS: Physics libraries & apps T: Tools for development VIS: Visualisation software
Name |
Version |
Description |
Software Group |
AnsysEM |
19.5 |
Ansys Electronics and Electrodynamics for research simulation. Provided for use by UBC researchers by a license through APSC. https://ansys.license.apsc.ubc.ca/ |
PHYS |
atlas |
3.10.2 |
Automatically Tuned Linear Algebra Software, generic shared ATLAS is an Homepage: http://math-atlas.sourceforge.net/ |
MATH |
bazel |
0.17.2 |
Bazel is Google's own build tool Homepage: https://www.bazel.io |
T |
beast1 |
1.10.4 |
BEAST is a cross-platform program for Bayesian analysis of molecular Homepage: http://beast.community/ |
BIO |
beast2 |
2.5.2 |
BEAST is a cross-platform program for Bayesian inference using MCMC of Homepage: http://beast2.org/ |
BIO |
boost |
1.54.0 |
Boost provides free peer-reviewed portable C++ source libraries, emphasizing libraries that work well with the C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. The Boost license encourages both commercial and non-commercial use. Homepage: https://www.boost.org/ |
T |
cmake |
3.15.0 |
A cross-platform, open-source build system. CMake is a family of tools Homepage: https://www.cmake.org |
T |
cuda |
10.0.130 |
CUDA is a parallel computing platform and programming model invented by NVIDIA. It enables dramatic increases in computing performance by Homepage: https://developer.nvidia.com/cuda-zone |
T |
cudnn |
7.5.1-10.0 |
NVIDIA cuDNN is a GPU-accelerated library of primitives for deep neural Homepage: https://developer.nvidia.com/cudnn |
T |
curl |
7.63.0 |
cURL is an open source command line tool and library for transferring Homepage: http://curl.haxx.se |
T |
ffmpeg |
4.1.1 |
FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video. Homepage: https://ffmpeg.org/ |
IO |
fftw |
3.3.8 |
FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications. Homepage: http://fftw.org/ |
MATH |
gcc |
5.4.0 / 9.1.0 |
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Homepage: https://gcc.gnu.org |
T |
git |
2.21.0 |
Git is a free and open source distributed version control system Homepage: http://git-scm.com |
T |
gnuplot |
5.2.5 / python 3.7.3 |
Gnuplot is a portable command-line driven graphing utility for Linux, Homepage: http://www.gnuplot.info |
VIS |
gromacs |
5.1.4 |
GROMACS (GROningen MAchine for Chemical Simulations) is a molecular Homepage: http://www.gromacs.org |
CHEM |
gsl |
2.5 |
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite. Homepage: https://www.gnu.org/software/gsl/ |
MATH |
hdf5 |
1.10.5 |
HDF5 is a data model, library, and file format for storing and managing Homepage: https://support.hdfgroup.org/HDF5/ |
IO |
intel-parallel-studio |
professional.2019.4 |
Intel Parallel Studio. Homepage: https://software.intel.com/en-us/intel-parallel-studio-xe |
T |
intel-mkl |
2019.3.199 |
Intel Math Kernel Library. |
T / MATH |
jdk |
12.0.2.10 |
The Java Development Kit (JDK) released by Oracle Corporation in the Homepage: http://www.oracle.com/technetwork/java/javase/downloads/index.html |
T |
lammps |
20190605 |
LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. This package uses patch releases, not stable release. See https://github.com/spack/spack/pull/5342 for a detailed discussion. Homepage: https://lammps.sandia.gov/ |
CHEM |
libx11 |
1.6.7 |
libX11 - Core X11 protocol client library. Homepage: https://www.x.org/ |
T |
libszip |
2.1.1 |
Szip is an implementation of the extended-Rice lossless compression algorithm. It provides lossless compression of scientific data, and is provided with HDF software products. |
T |
libxt |
1.1.5 |
libXt - X Toolkit Intrinsics library. |
T |
libxmu |
1.1.2 |
This library contains miscellaneous utilities and is not part of the Xlib standard. It contains routines which only use public interfaces so that it may be layered on top of any proprietary implementation of Xlib or Xt. |
T |
matlab |
2014a/2018b/2019b |
MATLAB (MATrix LABoratory) is a multi-paradigm numerical computing |
T |
mercurial |
4.4.1 / python 2.7.16 |
Mercurial is a free, distributed source control management tool. Homepage: https://www.mercurial-scm.org |
T |
mesa-glu |
9.0.0 |
This package provides the Mesa OpenGL Utility library. Homepage: https://www.mesa3d.org |
VIS |
mesa |
18.3.6 |
Mesa is an open-source implementation of the OpenGL specification - a Homepage: http://www.mesa3d.org |
VIS |
metis |
5.1.0 |
METIS is a set of serial programs for partitioning graphs, partitioning Homepage: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview |
MATH |
netcdf |
4.6.3 |
NetCDF is a set of software libraries and self-describing, machine- |
IO |
netcdf-cxx |
4.2 |
Deprecated C++ compatibility bindings for NetCDF. These do NOT read or |
IO |
netcdf-fortran |
4.4.5 |
Fortran interface for NetCDF4 |
IO |
netlib-lapack |
3.8.0 |
LAPACK version 3.X is a comprehensive FORTRAN library that does linear Homepage: http://www.netlib.org/lapack/ |
MATH |
netlib-xblas |
1.0.248 |
XBLAS is a reference implementation for extra precision BLAS. XBLAS is a Homepage: http://www.netlib.org/xblas |
MATH |
numactl |
2.0.12 |
NUMA support for Linux Homepage: http://oss.sgi.com/projects/libnuma/ |
T |
miniconda2 |
4.6.14 |
The minimalist bootstrap toolset for conda and Python2. Homepage: https://conda.io/miniconda.html |
T |
miniconda3 |
4.6.14 |
The minimalist bootstrap toolset for conda and Python3. Homepage: https://conda.io/miniconda.html |
T |
openblas |
0.3.6 |
OpenBLAS: An optimized BLAS library Homepage: http://www.openblas.net |
MATH |
openfoam-org |
3.0.1/5.0 |
OpenFOAM is a GPL-opensource C++ CFD-toolbox. The openfoam.org release is managed by the OpenFOAM Foundation Ltd as a licensee of the OPENFOAM trademark. This offering is not approved or endorsed by OpenCFD Ltd, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM trademark. Homepage: https://www.openfoam.org |
PHYS |
openmpi |
3.1.4 |
An open source Message Passing Interface implementation. The Open MPI Homepage: http://www.open-mpi.org |
M |
parallel |
20190222 |
GNU parallel is a shell tool for executing jobs in parallel using one or Homepage: http://www.gnu.org/software/parallel/ |
T |
parallel-netcdf |
1.11.1 |
PnetCDF (Parallel netCDF) is a high-performance parallel I/O library for Homepage: https://parallel-netcdf.github.io/ |
IO |
parmetis |
4.0.3 |
ParMETIS is an MPI-based parallel library that implements a variety of Homepage: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview |
MATH |
perl-uri |
1.72 |
Uniform Resource Identifiers (absolute and relative) |
T |
perl |
5.26.2 |
Perl 5 is a highly capable, feature-rich programming language with over Homepage: http://www.perl.org |
T |
petsc |
3.11.3 |
PETSc is a suite of data structures and routines for the scalable Homepage: http://www.mcs.anl.gov/petsc/index.html |
T |
picard |
2.19.0 |
Picard is a set of command line tools for manipulating high-throughput Homepage: http://broadinstitute.github.io/picard/ |
BIO |
plink |
1.07 |
PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Homepage: http://zzz.bwh.harvard.edu/plink/ |
BIO |
py-argparse |
1.4.0 / python 3.7.3 |
Python command-line parsing library. |
T |
py-cftime |
1.0.3.4 / python 2.7.16 / 3.6.8 / 3.7.3 |
Python library for decoding time units and variable values in a netCDF file conforming to the Climate and Forecasting (CF) netCDF conventions Homepage: https://pypi.org/project/cftime/ |
T |
py-jupyter-client |
4.4.0 / python 3.7.3 |
Jupyter protocol client APIs. Project Jupyter is a non-profit, open-source project, born out of the IPython Project in 2014 as it evolved to support interactive data science and scientific computing across all programming languages. Homepage: https://jupyter.org/ |
T |
py-jupyter-console |
5.2.0 / python 3.7.3 |
Jupyter Terminal Console. Project Jupyter is a non-profit, open-source project, born out of the IPython Project in 2014 as it evolved to support interactive data science and scientific computing across all programming languages. Homepage: https://jupyter.org/ |
T |
py-jupyter-core |
4.4.0 / python 3.7.3 |
Core Python Jupyter functionality. Project Jupyter is a non-profit, open-source project, born out of the IPython Project in 2014 as it evolved to support interactive data science and scientific computing across all programming languages. Homepage: https://jupyter.org/ |
T |
py-keras |
2.2.4 / python 3.7.3 |
Deep Learning library for Python. Convnets, recurrent neural networks, Homepage: http://keras.io |
AI |
py-keras-applications |
1.0.7 / python 3.7.3 |
Sample Deep Learning application in Keras. Keras depends on this package Homepage: http://keras.io |
AI |
py-keras-preprocessing |
1.0.9 / python 3.7.3 |
Utilities for working with image data, text data, and sequence data. Homepage: http://keras.io |
T |
py-mpi4py |
3.0.1 / python 3.7.3 |
This package provides Python bindings for the Message Passing Interface Homepage: https://pypi.python.org/pypi/mpi4py |
T |
py-netcdf4 |
1.4.2 / python 2.7.16/ 3.6.8/ 3.7.3 |
Python interface to the netCDF Library. Homepage: https://pypi.org/project/netCDF4/ |
T |
py-numpy |
1.16.4 / python 2.7.16 / 3.6.8 / 3.7.3 |
NumPy is the fundamental package for scientific computing with Python. Homepage: http://www.numpy.org/ |
MATH |
py-pandas |
0.24.2 / python 2.7.16 / 3.7.3 |
pandas is a Python package providing fast, flexible, and expressive data Homepage: http://pandas.pydata.org/ |
T |
py-pip |
19.0.3 / python 3.6.8 / 3.7.3 |
The PyPA recommended tool for installing Python packages. Homepage: https://pypi.python.org/pypi/pip |
T |
py-python-dateutil |
2.8.0 / python 2.7.16 / 3.7.3 |
Extensions to the standard Python datetime module. |
T |
py-pytz |
2018.4 / python 2.7.16 / 3.7.3 |
World timezone definitions, modern and historical. Homepage: https://pypi.org/project/pytz/ |
T |
py-scikit-learn |
0.21.2 / python 3.7.3 |
A set of python modules for machine learning and data mining. |
AI |
py-scipy |
1.2.1 / python 2.7.16 / 3.7.3 |
SciPy (pronounced "Sigh Pie") is a Scientific Library for Python. It Homepage: http://www.scipy.org/ |
MATH |
py-setuptools |
41.0.1 / python 2.7.16 / 3.6.8 / 3.7.3 |
A Python utility that aids in the process of downloading, building, Homepage: https://github.com/pypa/setuptools |
T |
py-six |
1.12.0 / python 2.7.16 / 3.7.3 |
Python 2 and 3 compatibility utilities. Homepage: https://pypi.org/project/six/ |
T |
py-theano |
1.0.4 / python 3.7.3 |
Optimizing compiler for evaluating mathematical expressions on CPUs and Homepage: http://deeplearning.net/software/theano/ |
T |
py-virtualenv-clone |
0.2.6 / python 2.7.16 / 3.6.8 / 3.7.3 |
A script for cloning a non-relocatable virtualenv. |
T |
py-virtualenv |
16.4.1 / python 2.7.16 / 3.6.8 / 3.7.3 |
virtualenv is a tool to create isolated Python environments. Homepage: https://virtualenv.pypa.io/ |
T |
python |
2.7.16 / 3.6.8 / 3.7.3 |
The Python programming language. Homepage: https://www.python.org/ |
T |
r-data-table |
1.11.8 / python 3.7.3 |
Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, |
T |
r-dplyr |
0.7.7 / python 3.7.3 |
A fast, consistent tool for working with data frame like objects, both Homepage: https://cran.r-project.org/package=dplyr |
T |
r-e1071 |
1.6.7 / python 3.7.3 |
Functions for latent class analysis, short time Fourier transform, fuzzy Homepage: https://cran.r-project.org/package=e1071 |
T |
r-ggplot2 |
2.2.1 / python 3.7.3 |
An implementation of the grammar of graphics in R. It combines the Homepage: http://ggplot2.org/ |
T |
r-nnet |
7.3.12 / python 3.7.3 |
Software for feed-forward neural networks with a single hidden layer, Homepage: http://www.stats.ox.ac.uk/pub/MASS4/ |
T |
r-plyr |
1.8.4 / python 3.7.3 |
A set of tools that solves a common set of problems: you need to break a Homepage: http://had.co.nz/plyr |
T |
r-randomforest |
4.6.12 / python 3.7.3 |
Classification and regression based on a forest of trees using random Homepage: https://www.stat.berkeley.edu/~breiman/RandomForests/ |
T |
r-rbokeh |
0.5.0 / python 3.7.3 |
R interface for creating plots in Bokeh. Bokeh by Continuum Analytics. Homepage: https://hafen.github.io/rbokeh |
T |
r-reshape |
0.8.7 / python 3.7.3 |
Flexibly restructure and aggregate data using just two functions: melt |
T |
r-reshape2 |
1.4.2 / python 3.7.3 |
Flexibly restructure and aggregate data using just two functions: melt Homepage: https://github.com/hadley/reshape |
T |
r-rpart-plot |
2.1.0 / python 3.7.3 |
Plot 'rpart' models. Extends plot.rpart() and text.rpart() in the |
T |
r-rpart |
4.1-11 / python 3.7.3 |
Recursive partitioning for classification, regression and survival Homepage: https://cran.r-project.org/package=rpart |
T |
r-shiny |
1.0.5 / python 3.7.3 |
Makes it incredibly easy to build interactive web applications with R. Homepage: http://shiny.rstudio.com/ |
T |
r-shinydashboard |
0.7.0 / python 3.7.3 |
Create Dashboards with 'Shiny' |
T |
r-tensora |
0.36 / python 3.7.3 |
The package provides convenience functions for advance linear algebra Homepage: https://cran.r-project.org/web/packages/tensorA/index.html |
T |
r |
3.6.0/3.6.2 / python 3.7.3 |
R is 'GNU S', a freely available language and environment for Homepage: https://www.r-project.org |
T |
singularity |
3.2.1 |
Singularity is a container technology focused on building portable Homepage: https://www.sylabs.io/singularity/ |
T |
spark |
2.3.0 |
Apache Spark is a fast and general engine for large-scale data Homepage: http://spark.apache.org |
T |
stacks |
2.3b |
Stacks is a software pipeline for building loci from short-read |
BIO |
supernova |
2.1.1 |
Supernova is a software package for de novo assembly from Chromium Homepage: https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome |
BIO |
superlu-dist |
6.1.1 |
A general purpose library for the direct solution of large, sparse, |
MATH |
xtensor |
0.20.7 |
Multi-dimensional arrays with broadcasting and lazy computing Homepage: http://quantstack.net/xtensor |
T |
xtensor-python |
0.23.1 / python 3.7.3 |
Python bindings for the xtensor C++ multi-dimensional array library Homepage: https://xtensor-python.readthedocs.io |
T |